organ = '187_gallbladder'
organ = '170_pancreas'
organ = '30325_left_adrenal_gland'
organ = '30324_right_adrenal_gland'
organ = '29193_first_lumbar_vertebra'
CWD = os.getcwd()
central_point = np.load(CWD + '/PatchedImage_v2/' + organ + '_' + regIfLinear +
'_central_point.npy')
ImageInfo = np.load(CWD + '/PreProcessing_v5/ImageInfo.npy')
ImageInfo = ImageInfo.item()
root = '/media/louis/Volume/ProgramWorkResult/VisercialMAS_ANT'
rawPredictDir = root + "/Result_Eigenfaces_KNN/PatchedImage/" + organ + '_' + regIfLinear + "/PCA_predict"
rawPredictlist = readTxtIntoList(rawPredictDir + "/FileListZoom.txt")
PredictDir = root + "/PredictRecovery/" + organ + '_' + regIfLinear + "_PredictRecovery"
if not os.path.exists(PredictDir):
subprocess.call('mkdir ' + '-p ' + PredictDir, shell=True)
predict_List = predictRecover(rawPredictlist, central_point, ImageInfo,
PredictDir)
WriteListtoFile(predict_List, PredictDir + "/FileList.txt")
#%%
# upsample
#root_dir = '/media/louis/Volume/ProgramWorkResult/MICCAI_2017_6_12/Full_Image'
#rawImageDir = root_dir + '/GC_Volumes_adjustment/Regtrans_linear'
#groundTruthDir = root_dir + '/GC_label_adjustment'+'/'+organ + '_'+ regIfLinear + '/Modification_Regtrans_linear'
RunRegistration = False
IFdownSample = True
IFNormalization = False
InterP = 0 # Bilinear interpolation would be order=1, nearest is order=0, and cubic is the default (order=3).
Regmode = 'nonlinear'
# output path
root_dir = '/media/data/louis/ProgramWorkResult/VisercialMAS_ANT'
root_image_dir = root_dir + '/Full_Image' + '/GC_Volumes_adjustment' # image root dir
root_label_dir = root_dir + '/Full_Image' + '/GC_label_adjustment' # image root dir
# Input path
data_folder = '/media/data/louis/ResearchData/visceral_used/GC_Volumes'
im_fns_raw = readTxtIntoList(data_folder + '/FileList.txt')
# adjust the GC original data.
Image_select = range(32) + range(33, 40)
'''
there is no "10000129_1_CTce_ThAb.nii.gz"
'''
im_fns = []
for i in Image_select:
im_fns.append(im_fns_raw[i])
#%%
sizeadjust_list = []
sizeadjust_image_dir = root_image_dir + '/sizeadjustment'
if not os.path.exists(sizeadjust_image_dir):
subprocess.call('mkdir ' + '-p ' + sizeadjust_image_dir, shell=True)
sitk.WriteImage(img, fn)
return outputlist
#%%
OrganPatch = False
LocalPatach = True
organ = '187_gallbladder'
constraint1 = 0.3
constraintgroundtruth = 0.02
#%%
#raw image
root = '/media/louis/Volume/ProgramWorkResult/MICCAI_2017_6_12'
image_dir = root + '/Patched_Image/GC_Volumes_patch' + '/' + organ + '_Imagepatch'
im_fns = readTxtIntoList(image_dir + '/' + 'FileList.txt')
normalizedImage_list = ImageNormlization(im_fns, image_dir)
WriteListtoFile(normalizedImage_list, image_dir + '/normalizedFileList.txt')
#%%
# predict dir
root_dir = '/media/louis/Volume/ProgramWorkResult/MICCAI_2017_6_12/Result_Eigenfaces_KNN/PatchedImage'
if OrganPatch == True:
result_dir_pre = root_dir + '/' + organ + '/PCA_predict'
elif LocalPatach == True:
result_dir_pre = root_dir + '/' + organ + 'LocalPatch' + '/PCA_predict'
else:
raise ValueError('please choose the patch pattern')
print 'Results will be stored in:', result_dir_pre
if not os.path.exists(result_dir_pre):